McCarthy, KRachida, SYousif, MNdlovu, NHoward, WMoonsamy, SIwu-Jala, CIsmael, ASchaefer, Lisa MLe Roux, Wouter J2022-05-062022-05-062021-12McCarthy, K., Rachida, S., Yousif, M., Ndlovu, N., Howard, W., Moonsamy, S., Iwu-Jala, C. & Ismael, A. et al. 2021. Wastewater-based genomic and epidemiological monitoring of SARS-CoV-2, South Africa, 2020-2021. http://hdl.handle.net/10204/12394 .http://hdl.handle.net/10204/12394Findings from wastewater-based epidemiology (WBE) surveillance of SARS-CoV-2 are increasingly used to monitor the epidemiology of SARS-CoV-2. We report on the findings from the South African Collaboration COVID-19 Environmental Surveillance System (SACCESS) laboratories and compare these with clinically obtained data. Wastewater grab or passive samples and underwent concentration, RNA extraction, reverse-transcriptase-polymerase chain reaction (RT-PCR) detection and quantification of SARS-CoV-2. Following whole genome amplicon-based sequencing, nonsynonymous mutations in the spike protein specific to variants of concern (VOCs) were identified. Quantitative RNA concentrations in genome copies/mL and the read-frequencies of lineage-specific single nucleotide polymorphisms (SNPs) in the spike protein of SARS-CoV-2 were plotted alongside official case load and SARS-Cov-2 lineage distribution by epidemiological week (provided by NICD SARS-CoV-2 epidemiology team and the Centre for Respiratory Diseases and Meningitis of the NICD). Results from 95 wastewater treatment plants (WWTPs) across 9 provinces and all eight metropolitan areas of South Africa were collected weekly, biweekly or monthly from June 2020-October 2021 illustrate that increases and decreases in SARS-CoV-2 concentrations at all sites corresponded to metro-specific timing of the peak and post-peak decline in clinical cases. Increases in SARS-CoV-2 concentrations consistently preceded increases in clinical cases. In 18 WWTPs genomic analysis detected SNPs corresponding to prevalent VOCs and documented the change from beta to delta variant over the third SARS-CoV-2 wave.FulltextenMolecular epidemiologyPublic healthSARS-CoV-2Wastewater-based epidemiologyConference PresentationMcCarthy, K., Rachida, S., Yousif, M., Ndlovu, N., Howard, W., Moonsamy, S., ... Le Roux, W. J. (2021). Wastewater-based genomic and epidemiological monitoring of SARS-CoV-2, South Africa, 2020-2021. http://hdl.handle.net/10204/12394McCarthy, K, S Rachida, M Yousif, N Ndlovu, W Howard, S Moonsamy, C Iwu-Jala, A Ismael, Lisa M Schaefer, and Wouter J Le Roux. "Wastewater-based genomic and epidemiological monitoring of SARS-CoV-2, South Africa, 2020-2021." <i>The 1st International Conference on Public Health in Africa (CPHIA 2021), Addis Ababa, Ethiopia, 16 December 2021</i> (2021): http://hdl.handle.net/10204/12394McCarthy K, Rachida S, Yousif M, Ndlovu N, Howard W, Moonsamy S, et al, Wastewater-based genomic and epidemiological monitoring of SARS-CoV-2, South Africa, 2020-2021; 2021. http://hdl.handle.net/10204/12394 .TY - Conference Presentation AU - McCarthy, K AU - Rachida, S AU - Yousif, M AU - Ndlovu, N AU - Howard, W AU - Moonsamy, S AU - Iwu-Jala, C AU - Ismael, A AU - Schaefer, Lisa M AU - Le Roux, Wouter J AB - Findings from wastewater-based epidemiology (WBE) surveillance of SARS-CoV-2 are increasingly used to monitor the epidemiology of SARS-CoV-2. We report on the findings from the South African Collaboration COVID-19 Environmental Surveillance System (SACCESS) laboratories and compare these with clinically obtained data. Wastewater grab or passive samples and underwent concentration, RNA extraction, reverse-transcriptase-polymerase chain reaction (RT-PCR) detection and quantification of SARS-CoV-2. Following whole genome amplicon-based sequencing, nonsynonymous mutations in the spike protein specific to variants of concern (VOCs) were identified. Quantitative RNA concentrations in genome copies/mL and the read-frequencies of lineage-specific single nucleotide polymorphisms (SNPs) in the spike protein of SARS-CoV-2 were plotted alongside official case load and SARS-Cov-2 lineage distribution by epidemiological week (provided by NICD SARS-CoV-2 epidemiology team and the Centre for Respiratory Diseases and Meningitis of the NICD). Results from 95 wastewater treatment plants (WWTPs) across 9 provinces and all eight metropolitan areas of South Africa were collected weekly, biweekly or monthly from June 2020-October 2021 illustrate that increases and decreases in SARS-CoV-2 concentrations at all sites corresponded to metro-specific timing of the peak and post-peak decline in clinical cases. Increases in SARS-CoV-2 concentrations consistently preceded increases in clinical cases. In 18 WWTPs genomic analysis detected SNPs corresponding to prevalent VOCs and documented the change from beta to delta variant over the third SARS-CoV-2 wave. DA - 2021-12 DB - ResearchSpace DP - CSIR J1 - The 1st International Conference on Public Health in Africa (CPHIA 2021), Addis Ababa, Ethiopia, 16 December 2021 KW - Molecular epidemiology KW - Public health KW - SARS-CoV-2 KW - Wastewater-based epidemiology LK - https://researchspace.csir.co.za PY - 2021 T1 - Wastewater-based genomic and epidemiological monitoring of SARS-CoV-2, South Africa, 2020-2021 TI - Wastewater-based genomic and epidemiological monitoring of SARS-CoV-2, South Africa, 2020-2021 UR - http://hdl.handle.net/10204/12394 ER -25610